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Yorodumi- PDB-4chm: Structure of Inner Membrane Complex (IMC) Sub-compartment Protein... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4chm | ||||||
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Title | Structure of Inner Membrane Complex (IMC) Sub-compartment Protein 1 (ISP1) from Toxoplasma gondii | ||||||
Components | IMC SUB-COMPARTMENT PROTEIN ISP1 | ||||||
Keywords | CELL CYCLE / CELL DIVISION / ENDODYOGENY / PLECKSTRIN HOMOLOGY (PH) FOLD | ||||||
Function / homology | ISP1 C-terminal / ISP1 C-terminal / Pleckstrin-homology domain (PH domain)/Phosphotyrosine-binding domain (PTB) / PH-domain like / PH-like domain superfamily / Roll / Mainly Beta / IMC sub-compartment protein ISP1 / IMC sub-compartment protein ISP1 Function and homology information | ||||||
Biological species | TOXOPLASMA GONDII (eukaryote) | ||||||
Method | X-RAY DIFFRACTION / SAD / Resolution: 2.1 Å | ||||||
Authors | Tonkin, M.L. / Beck, J.R. / Bradley, P.J. / Boulanger, M.J. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2014 Title: The Inner Membrane Complex Sub-Compartment Proteins Critical for Replication of the Apicomplexan Parasite Toxoplasma Gondii Adopt a Pleckstrin Homology Fold Authors: Tonkin, M.L. / Beck, J.R. / Bradley, P.J. / Boulanger, M.J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4chm.cif.gz | 109.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4chm.ent.gz | 89.9 KB | Display | PDB format |
PDBx/mmJSON format | 4chm.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ch/4chm ftp://data.pdbj.org/pub/pdb/validation_reports/ch/4chm | HTTPS FTP |
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-Related structure data
-Links
-Assembly
Deposited unit |
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Unit cell |
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-Components
#1: Protein | Mass: 13844.036 Da / Num. of mol.: 4 / Fragment: PH FOLD CORE DOMAIN, RESIDUES 58-176 Source method: isolated from a genetically manipulated source Source: (gene. exp.) TOXOPLASMA GONDII (eukaryote) / Strain: ME49 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): CODON PLUS / References: UniProt: S8GCI7, UniProt: B9PKK4*PLUS #2: Chemical | ChemComp-SO4 / #3: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 2.44 Å3/Da / Density % sol: 49.56 % / Description: NONE |
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Crystal grow | Details: 0.1 M BIS-TRIS PH 5.5, 25% PEG 3350 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU MICROMAX-002 / Wavelength: 1.542 |
Detector | Type: RIGAKU R-AXIS IV / Detector: IMAGE PLATE / Details: OSMIC BLUE |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.542 Å / Relative weight: 1 |
Reflection | Resolution: 2.1→29.09 Å / Num. obs: 33884 / % possible obs: 99.9 % / Observed criterion σ(I): 2 / Redundancy: 4.7 % / Rmerge(I) obs: 0.07 / Net I/σ(I): 16.3 |
Reflection shell | Resolution: 2.1→2.21 Å / Redundancy: 4.8 % / Rmerge(I) obs: 0.38 / Mean I/σ(I) obs: 4.5 / % possible all: 100 |
-Processing
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Refinement | Method to determine structure: SAD Starting model: NONE Resolution: 2.1→28.15 Å / Cor.coef. Fo:Fc: 0.944 / Cor.coef. Fo:Fc free: 0.916 / SU B: 5.2 / SU ML: 0.139 / Cross valid method: THROUGHOUT / ESU R: 0.229 / ESU R Free: 0.198 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 28.985 Å2
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Refinement step | Cycle: LAST / Resolution: 2.1→28.15 Å
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